[phenixbb] Fwd: Really good stats... Unreal!??

Pavel Afonine pafonine at lbl.gov
Tue Oct 4 17:34:19 PDT 2011


Hi Yuri,

> So I am done refining a structure with around 760 residues in the 
> model to a resolution of 2.29A. Rwork 0.18 Rfree 0.24
> RMSD angle 1.1 Bond 0.008, clashscore 28.

Looks ok to me, with some room for improvement (Rfree-Rwork gap, 
clash-score).

> As a I last round I ran optmize_weights and got some interesting numbers.
> Rwork 0.17 Rfree 0.23
> RMSD Angle 0.68! Bond 0.003! clashscore 10.2

Looks even better! That's what weight optimization was supposed to do:
http://www.phenix-online.org/newsletter/
("Improved target weight optimization in phenix.refine")

Looking at R-factors for structures in PDB that are similar to yours:

Histogram of Rwork for models in PDB at resolution 2.19-2.39 A:
      0.126 - 0.147      : 29
      0.147 - 0.168      : 245
      0.168 - 0.189      : 941 <<<< your structure
      0.189 - 0.210      : 1613
      0.210 - 0.232      : 1394
      0.232 - 0.253      : 531
      0.253 - 0.274      : 123
      0.274 - 0.295      : 11
      0.295 - 0.316      : 1
      0.316 - 0.337      : 4
Histogram of Rfree for models in PDB at resolution 2.19-2.39 A:
      0.165 - 0.188      : 31
      0.188 - 0.211      : 220
      0.211 - 0.235      : 848 <<<< your structure
      0.235 - 0.258      : 1692
      0.258 - 0.281      : 1459
      0.281 - 0.304      : 522
      0.304 - 0.328      : 94
      0.328 - 0.351      : 19
      0.351 - 0.374      : 6
      0.374 - 0.397      : 1
Histogram of Rfree-Rwork for all model in PDB at resolution 2.19-2.39 A:
      0.001 - 0.011      : 51
      0.011 - 0.021      : 170
      0.021 - 0.031      : 509
      0.031 - 0.041      : 944
      0.041 - 0.050      : 1238
      0.050 - 0.060      : 1017 <<<< your structure
      0.060 - 0.070      : 574
      0.070 - 0.080      : 214
      0.080 - 0.090      : 110
      0.090 - 0.100      : 65
Number of structures considered: 4892

Well, looks like just average!

Pavel



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